Publikácie

@article{Forgacova2023,

title = {Evaluation and limitations of different approaches among COVID-19 fatal cases using whole-exome sequencing data},

author = {N. Forgacova and Z. Holesova and R. Hekel and T. Sedlackova and Z. Pos and L. Krivosikova and P. Janega and K. M. Kuracinova and P. Babal and P. Radvak and J. Radvanszky and J. Gazdarica and J. Budis and T. Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85146101670&doi=10.1186%2fs12864-022-09084-5&partnerID=40&md5=d25846b50ef1ee4668a13ebd7d02bb47},

doi = {10.1186/s12864-022-09084-5},

issn = {14712164},

year  = {2023},

date = {2023-01-01},

urldate = {2023-01-01},

journal = {BMC Genomics},

volume = {24},

number = {1},

publisher = {BioMed Central Ltd},

abstract = {Background: COVID-19 caused by the SARS-CoV-2 infection may result in various disease symptoms and severity, ranging from asymptomatic, through mildly symptomatic, up to very severe and even fatal cases. Although environmental, clinical, and social factors play important roles in both susceptibility to the SARS-CoV-2 infection and progress of COVID-19 disease, it is becoming evident that both pathogen and host genetic factors are important too. In this study, we report findings from whole-exome sequencing (WES) of 27 individuals who died due to COVID-19, especially focusing on frequencies of DNA variants in genes previously associated with the SARS-CoV-2 infection and the severity of COVID-19. Results: We selected the risk DNA variants/alleles or target genes using four different approaches: 1) aggregated GWAS results from the GWAS Catalog; 2) selected publications from PubMed; 3) the aggregated results of the Host Genetics Initiative database; and 4) a commercial DNA variant annotation/interpretation tool providing its own knowledgebase. We divided these variants/genes into those reported to influence the susceptibility to the SARS-CoV-2 infection and those influencing the severity of COVID-19. Based on the above, we compared the frequencies of alleles found in the fatal COVID-19 cases to the frequencies identified in two population control datasets (non-Finnish European population from the gnomAD database and genomic frequencies specific for the Slovak population from our own database). When compared to both control population datasets, our analyses indicated a trend of higher frequencies of severe COVID-19 associated risk alleles among fatal COVID-19 cases. This trend reached statistical significance specifically when using the HGI-derived variant list. We also analysed other approaches to WES data evaluation, demonstrating its utility as well as limitations. Conclusions: Although our results proved the likely involvement of host genetic factors pointed out by previous studies looking into severity of COVID-19 disease, careful considerations of the molecular-testing strategies and the evaluated genomic positions may have a strong impact on the utility of genomic testing. © 2023, The Author(s).},

note = {cited By 0},

keywords = {Non-invasive prenatal testing, Sars-cov-2},

pubstate = {published},

tppubtype = {article}

}

@article{Radvánszka2022,

title = {Sequential development of several RT-qPCR tests using LNA nucleotides and dual probe technology to differentiate SARS-CoV-2 from influenza A and B},

author = {M. Radvánszka and E. D. Paul and R. Hajdu and K. Boršová and V. Kováčová and P. Putaj and S. Bírová and I. Čirková and M. Čarnecký and K. Buranovská and A. Szobi and N. Vojtaššáková and D. Drobná and V. Čabanová and M. Sláviková and M. Ličková and V. Vaňová and S. Fumačová Havlíková and Ľ. Lukáčiková and I. Kajanová and J. Koči and D. Rusňáková and T. Sedláčková and K. E. A. Max and T. Tuschl and T. Szemes and B. Klempa and P. Čekan},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85126870587&doi=10.1111%2f1751-7915.14031&partnerID=40&md5=6bfbb30ff38aa6d088d9ffd526e1762f},

doi = {10.1111/1751-7915.14031},

issn = {17517907},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Microbial Biotechnology},

publisher = {John Wiley and Sons Ltd},

abstract = {Sensitive and accurate RT-qPCR tests are the primary diagnostic tools to identify SARS-CoV-2-infected patients. While many SARS-CoV-2 RT-qPCR tests are available, there are significant differences in test sensitivity, workflow (e.g. hands-on-time), gene targets and other functionalities that users must consider. Several publicly available protocols shared by reference labs and public health authorities provide useful tools for SARS-CoV-2 diagnosis, but many have shortcomings related to sensitivity and laborious workflows. Here, we describe a series of SARS-CoV-2 RT-qPCR tests that are originally based on the protocol targeting regions of the RNA-dependent RNA polymerase (RdRp) and envelope (E) coding genes developed by the Charité Berlin. We redesigned the primers/probes, utilized locked nucleic acid nucleotides, incorporated dual probe technology and conducted extensive optimizations of reaction conditions to enhance the sensitivity and specificity of these tests. By incorporating an RNase P internal control and developing multiplexed assays for distinguishing SARS-CoV-2 and influenza A and B, we streamlined the workflow to provide quicker results and reduced consumable costs. Some of these tests use modified enzymes enabling the formulation of a room temperature-stable master mix and lyophilized positive control, thus increasing the functionality of the test and eliminating cold chain shipping and storage. Moreover, a rapid, RNA extraction-free version enables high sensitivity detection of SARS-CoV-2 in about an hour using minimally invasive, self-collected gargle samples. These RT-qPCR assays can easily be implemented in any diagnostic laboratory and can provide a powerful tool to detect SARS-CoV-2 and the most common seasonal influenzas during the vaccination phase of the pandemic. © 2022 Multiplex DX, S.R.O. Microbial Biotechnology published by Society for Applied Microbiology and John Wiley & Sons Ltd.},

keywords = {Sars-cov-2, Viruses},

pubstate = {published},

tppubtype = {article}

}

@article{Rusňáková2022,

title = {Systematic Genomic Surveillance of SARS-CoV-2 Virus on Illumina Sequencing Platforms in the Slovak Republic—One Year Experience},

author = {D. Rusňáková and T. Sedláčková and P. Radvák and M. Böhmer and P. Mišenko and J. Budiš and S. Bokorová and N. Lipková and M. Forgáčová-Jakúbková and T. Sládeček and J. Sitarčík and W. Krampl and M. Gažiová and A. Kaliňáková and E. Staroňová and E. Tichá and T. Vrábľová and L. Ševčíková and B. Kotvasová and L. Maďarová and S. Feiková and K. Beňová and L. Reizigová and Z. Onderková and D. Ondrušková and D. Loderer and M. Škereňová and Z. Danková and K. Janíková and E. Halašová and E. Nováková and J. Turňa and T. Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85141590744&doi=10.3390%2fv14112432&partnerID=40&md5=ae8783f0d6a244a1eeea0fb3d17f7230},

doi = {10.3390/v14112432},

issn = {19994915},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Viruses},

volume = {14},

number = {11},

publisher = {MDPI},

abstract = {To explore a genomic pool of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the pandemic, the Ministry of Health of the Slovak Republic formed a genomics surveillance workgroup, and the Public Health Authority of the Slovak Republic launched a systematic national epidemiological surveillance using whole-genome sequencing (WGS). Six out of seven genomic centers implementing Illumina sequencing technology were involved in the national SARS-CoV-2 virus sequencing program. Here we analyze a total of 33,024 SARS-CoV-2 isolates collected from the Slovak population from 1 March 2021, to 31 March 2022, that were sequenced and analyzed in a consistent manner. Overall, 28,005 out of 30,793 successfully sequenced samples met the criteria to be deposited in the global GISAID database. During this period, we identified four variants of concern (VOC)—Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2) and Omicron (B.1.1.529). In detail, we observed 165 lineages in our dataset, with dominating Alpha, Delta and Omicron in three major consecutive incidence waves. This study aims to describe the results of a routine but high-level SARS-CoV-2 genomic surveillance program. Our study of SARS-CoV-2 genomes in collaboration with the Public Health Authority of the Slovak Republic also helped to inform the public about the epidemiological situation during the pandemic. © 2022 by the authors.},

keywords = {Sars-cov-2, Viruses},

pubstate = {published},

tppubtype = {article}

}